	US 12,227,737 B2
	Cancer detection and classification using methylome analysis
Daniel Diniz De Carvalho, Toronto (CA); Shu Yi Shen, Markham (CA); Rajat Singhania, Toronto (CA); Scott Victor Bratman, Toronto (CA); and Ankur Ravinarayana Chakravarthy, Toronto (CA)
Assigned to University Health Network, Toronto (CA); and Sinai Health System, Toronto (CA)
Filed by University Health Network, Toronto (CA); and Sinai Health System, Toronto (CA)
Filed on Dec. 2, 2022, as Appl. No. 18/061,273.
Application 18/061,273 is a continuation in part of application No. 16/630,299, previously published as PCT/CA2018/000141, filed on Jul. 11, 2018.
Claims priority of provisional application 62/531,527, filed on Jul. 12, 2017.
Prior Publication US 2023/0203473 A1, Jun. 29, 2023
Int. Cl. C12N 15/10 (2006.01); C12Q 1/6804 (2018.01); C12Q 1/6806 (2018.01); C12Q 1/6886 (2018.01); C40B 30/04 (2006.01); G01N 33/53 (2006.01)

CPC C12N 15/1003 (2013.01) [C12N 15/10 (2013.01); C12N 15/1093 (2013.01); C12Q 1/6804 (2013.01); C12Q 1/6806 (2013.01); G01N 33/5308 (2013.01); C12Q 1/6886 (2013.01); C12Q 2600/154 (2013.01); C40B 30/04 (2013.01)]

27 Claims

1. A method, comprising:

(a) subjecting a plurality of nucleic acid molecules generated from a cell-free deoxynucleic acid (cfDNA) sample of a subject to sequencing to yield a plurality of sequencing reads, wherein said plurality of nucleic acid molecules is generated by subjecting nucleic acid molecules derived from said cfDNA sample to enrichment through immunoprecipitation of one or more methylated regions of said nucleic acid molecules;

(b) computer processing said plurality of sequencing reads to generate a methylation profile for said plurality of nucleic acid molecules; and

(c) computer processing said methylation profile to determine that said subject has or is at risk of having a cancer at an area under a receiver operating characteristic curve (AUROC) of at least about 94%.